Human immunodeficiency virus (HIV) is the human retrovirus associated with AIDS (acquired immune deficiency syndrome), and SIV its simian counterpart. Three main groups of primate lentivirus are known, designated Human immunodeficiency virus 1 (HIV-1), Human immunodeficiency virus 2 (HIV-2)/Simian immunodeficiency virus - mac (SIVMAC)/Simian immunodeficiency virus - sm (SIVSM) and Simian immunodeficiency virus - agm (SIVAGM). Simian immunodeficiency virus - mnd (SIVMND) has been suggested to represent a fourth distinct group [[cite:PUB00004048]]. These groups are believed to have diverged from a common ancestor long before the spread of AIDS in humans. Genetic variation in HIV-1 and HIV-2 has been studied extensively, and the nucleotide sequences reported for several strains [[cite:PUB00000018]].
ORF analysis has revealed two open reading frames, yielding the so-called R- and X-ORF proteins, which show a high degree of sequence similarity.
\r\n\r\nVpx plays a role in nuclear translocation of the viral pre-integration complex (PIC) and is thus required for the virus to infect non-dividing cells. Vpr also plays a role in nuclear translocation of the (PIC) and may target specific host proteins for degradation by the 26S proteasome. It acts by associating with the cellular CUL4A-DDB1 E3 ligase complex through direct interaction with host VPRPB/DCAF-1. This would result in cell cycle arrest or apoptosis in infected cells, creating a favourable environment for maximizing viral expression and production by rendering the HIV-1 LTR transcription more active.
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000037","name":"SsrA-binding protein","source_database":"interpro","type":"family","integrated":null,"member_databases":{"cdd":{"cd09294":"Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs"},"panther":{"PTHR30308":"TMRNA-BINDING COMPONENT OF TRANS-TRANSLATION TAGGING COMPLEX"},"hamap":{"MF_00023":"SsrA-binding protein [smpB]"},"ncbifam":{"TIGR00086":"SsrA-binding protein"},"pfam":{"PF01668":"SmpB protein"}},"go_terms":[{"identifier":"GO:0003723","name":"RNA binding","category":{"code":"F","name":"molecular_function"}}]},"extra_fields":{"description":[{"text":"This entry represents SsrA-binding protein (aka small protein B or SmpB), which is a unique RNA-binding protein that is conserved throughout the bacterial kingdom and is an essential component of the SsrA quality-control system. Tight recognition of codon-anticodon pairings by the ribosome ensures the accuracy and fidelity of protein synthesis. In eubacteria, translational surveillance and ribosome rescue are performed by the 'tmRNA-SmpB' system (transfer messenger RNA-small protein B). SmpB binds specifically to the ssrA RNA (tmRNA) and is required for stable association of ssrA with ribosomes. SsrA RNA recognises ribosomes stalled on defective messages and acts to mediate the addition of a short peptide tag to the C terminus of the partially synthesised nascent polypeptide chain. Within a stalled ribosome, SmpB interacts with the three universally conserved bases G530, A1492 and A1493 that form the 30S subunit decoding centre, in which canonical codon-anticodon pairing occurs [[cite:PUB00045920]]. The SsrA-tagged protein is then degraded by C-terminal-specific proteases. Formation of an SmpB-SsrA complex appears to be critical in mediating SsrA activity after aminoacylation with alanine but prior to the transpeptidation reaction that couples this alanine to the nascent chain [[cite:PUB00006449]]. The SmpB protein has functional and structural similarities with initiation factor 1, and is proposed to be a functional mimic of the pairing between a codon and an anticodon.
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000043","name":"Adenosylhomocysteinase-like","source_database":"interpro","type":"family","integrated":null,"member_databases":{"cdd":{"cd00401":"S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains"},"smart":{"SM00996":"S-adenosyl-L-homocysteine hydrolase"},"pirsf":{"PIRSF001109":"Adenosylhomocysteine hydrolase, SAHH type"},"hamap":{"MF_00563":"S-inosyl-L-homocysteine hydrolase [ahcY]"},"panther":{"PTHR23420":"ADENOSYLHOMOCYSTEINASE"},"pfam":{"PF05221":"S-adenosyl-L-homocysteine hydrolase"},"ncbifam":{"TIGR00936":"adenosylhomocysteinase"}},"go_terms":null},"extra_fields":{"description":[{"text":"Adenosylhomocysteinase (S-adenosyl-L-homocysteine hydrolase, [ec:3.3.1.1]) (AdoHcyase) is an enzyme of the activated methyl cycle, responsible for the reversible hydration of S-adenosyl-L-homocysteine into adenosine and homocysteine. This enzyme is ubiquitous, highly conserved, and may play a key role in the regulation of the intracellular concentration of adenosylhomocysteine. AdoHcyase requires NAD+ as a cofactor and contains a central glycine-rich region which is thought to be involved in NAD-binding. Since AdoHyc is a potent inhibitor of S-adenosyl-L-methionine dependent methyltransferases, AdoHycase plays a critical role in the modulation of the activity of various methyltransferases. The enzyme forms homotetramers, with each monomer binding one molecule of NAD+ [[cite:PUB00021119], [cite:PUB00038377], [cite:PUB00079516], [cite:PUB00079517]].
","llm":false,"checked":false,"updated":false},{"text":"This family also includes S-adenosylhomocysteine hydrolase-like 1 (Ahcyl1), also known as IRBIT, and S-adenosylhomocysteine hydrolase-like protein 2 (Ahcyl2). Ahcyl1/IRBIT was shown to interact with inositol 1,4,5-trisphosphate receptors (IP3Rs), which function as intracellular Ca(2+) channels, and suppresses IP3 binding of IP3R [[cite:PUB00083401], [cite:PUB00083402]]. By competing with IP3, it modulates the threshold IP3 concentration required for the activation of the receptor [[cite:PUB00083401]]. Further studies indicate that Ahcyl1/IRBIT is in fact a multifunctional protein that regulates several ion channels and ion transporters [[cite:PUB00083432], [cite:PUB00083433]]. Despite its homology to S-adenosylhomocysteine hydrolases, Ahcyl1 has neither enzyme activity nor any effects on the enzyme activity of S-adenosylhomocysteine hydrolase [[cite:PUB00083397]]. Ahcyl2 lacks binding activity to IP3R [[cite:PUB00083418]]. Ahcyl2 upregulates NBCe1-B, which plays an important role in intracellular pH regulation [[cite:PUB00083434]].
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000054","name":"Large ribosomal subunit protein eL31","source_database":"interpro","type":"family","integrated":null,"member_databases":{"cdd":{"cd00463":"Eukaryotic/archaeal ribosomal protein L31"},"smart":{"SM01380":"Ribosomal_L31e"},"hamap":{"MF_00410":"Large ribosomal subunit protein eL31 [rpl31e]"},"pfam":{"PF01198":"Ribosomal protein L31e"},"panther":{"PTHR10956":"60S RIBOSOMAL PROTEIN L31"}},"go_terms":[{"identifier":"GO:0003735","name":"structural constituent of ribosome","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0006412","name":"translation","category":{"code":"P","name":"biological_process"}},{"identifier":"GO:0005840","name":"ribosome","category":{"code":"C","name":"cellular_component"}}]},"extra_fields":{"description":[{"text":"A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 87 to 128 amino-acid residues. This family consists of:
\n\nRibosomal protein eL31, which is present in archaea and eukaryotes, binds the 23S rRNA and is one of six protein components encircling the polypeptide exit tunnel. It is a component of the eukaryotic 60S (large) ribosomal subunit, and the archaeal 50S (large) ribosomal subunit [[cite:PUB00079812], [cite:PUB00079483], [cite:PUB00079813], [cite:PUB00079814], [cite:PUB00079524], [cite:PUB00007070], [cite:PUB00007068], [cite:PUB00079815], [cite:PUB00079816], [cite:PUB00079817], [cite:PUB00037574], [cite:PUB00079818], [cite:PUB00079819], [cite:PUB00079820], [cite:PUB00028498], [cite:PUB00009424], [cite:PUB00030402], [cite:PUB00079821], [cite:PUB00038013]].
","llm":false,"checked":false,"updated":false},{"text":"Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA, and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid of the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [[cite:PUB00007068], [cite:PUB00007069]]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 consists of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to: the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.
\n\nMany ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waals' contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way, proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA-based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [[cite:PUB00007069], [cite:PUB00007070]].
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000077","name":"Large ribosomal subunit protein eL39","source_database":"interpro","type":"family","integrated":null,"member_databases":{"hamap":{"MF_00629":"Large ribosomal subunit protein eL39 [rpl39e]"},"pfam":{"PF00832":"Ribosomal L39 protein"}},"go_terms":[{"identifier":"GO:0003735","name":"structural constituent of ribosome","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0006412","name":"translation","category":{"code":"P","name":"biological_process"}},{"identifier":"GO:0005840","name":"ribosome","category":{"code":"C","name":"cellular_component"}}]},"extra_fields":{"description":[{"text":"A number of eukaryotic and archaebacterial large subunit ribosomal proteins can be grouped on the basis of sequence similarities. This entry represents the large ribosomal subunit protein eL39, of about 50 residues long, being the smallest protein of eukaryotic-type ribosomes. In mammals, eL39 has been described as the RNA-binding component of the large ribosomal subunit [[cite:PUB00151099], [cite:PUB00151098]].
","llm":false,"checked":false,"updated":false},{"text":"Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA, and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid of the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [[cite:PUB00007068], [cite:PUB00007069]]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 consists of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to: the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.
\n\nMany ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waals' contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way, proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA-based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [[cite:PUB00007069], [cite:PUB00007070]].
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000085","name":"Holliday junction branch migration complex subunit RuvA","source_database":"interpro","type":"family","integrated":null,"member_databases":{"hamap":{"MF_00031":"Holliday junction branch migration complex subunit RuvA [ruvA]"},"ncbifam":{"TIGR00084":"Holliday junction branch migration protein RuvA"}},"go_terms":[{"identifier":"GO:0003678","name":"DNA helicase activity","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0006281","name":"DNA repair","category":{"code":"P","name":"biological_process"}},{"identifier":"GO:0006310","name":"DNA recombination","category":{"code":"P","name":"biological_process"}}]},"extra_fields":{"description":[{"text":"In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA, known as Holliday junction branch migration complex subunit RuvA, specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure [[cite:PUB00013198]]. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB.
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000093","name":"DNA recombination protein RecR","source_database":"interpro","type":"family","integrated":null,"member_databases":{"panther":{"PTHR30446":"RECOMBINATION PROTEIN RECR"},"hamap":{"MF_00017":"Recombination protein RecR [recR]"},"ncbifam":{"TIGR00615":"recombination mediator RecR"}},"go_terms":[{"identifier":"GO:0003677","name":"DNA binding","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0046872","name":"metal ion binding","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0006281","name":"DNA repair","category":{"code":"P","name":"biological_process"}},{"identifier":"GO:0006310","name":"DNA recombination","category":{"code":"P","name":"biological_process"}}]},"extra_fields":{"description":[{"text":"The bacterial protein RecR is an important regulator in the RecFOR homologous recombination pathway during DNA repair [[cite:PUB00004365], [cite:PUB00032061], [cite:PUB00101156], [cite:PUB00064122]]. It acts with RecF and RecO forming a complex that facilitates the loading of RecA onto ssDNA [[cite:PUB00101156], [cite:PUB00064122]]. RecR is a zinc metalloprotein consisting of a N-terminal helix-hairpin-helix (HhH) motif, a middle region containing a zinc finger motif and a Toprim domain, and a C-terminal domain comprising a divergent Walker B motif and a C-terminal helix [[cite:PUB00101156], [cite:PUB00064122]].
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000100","name":"Ribonuclease P","source_database":"interpro","type":"family","integrated":null,"member_databases":{"panther":{"PTHR33992":"RIBONUCLEASE P PROTEIN COMPONENT"},"hamap":{"MF_00227":"Ribonuclease P protein component [rnpA]"},"ncbifam":{"TIGR00188":"ribonuclease P protein component, bacterial type"},"pfam":{"PF00825":"Ribonuclease P"}},"go_terms":[{"identifier":"GO:0000049","name":"tRNA binding","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0004526","name":"ribonuclease P activity","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0008033","name":"tRNA processing","category":{"code":"P","name":"biological_process"}}]},"extra_fields":{"description":[{"text":"Ribonuclease P ([ec:3.1.26.5]) (RNase P) [[cite:PUB00002604], [cite:PUB00002589], [cite:PUB00004402]] is a site specific endonuclease that generates mature tRNAs by catalysing the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. In bacteria RNase P is known to be composed of two components: a large RNA (about 400 base pairs) encoded by rnpB, and a small protein (119 to 133 amino acids) encoded by rnpA. The RNA moiety of RNase P carries the catalytic activity; the protein component plays an auxiliary, but essential, role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. The sequence of rnpA is not highly conserved, however there is, in the central part of the protein, a conserved basic region.
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000114","name":"Large ribosomal subunit protein uL16, bacteria","source_database":"interpro","type":"family","integrated":null,"member_databases":{"hamap":{"MF_01342":"Large ribosomal subunit protein uL16 [rplP]"},"panther":{"PTHR12220":"50S/60S RIBOSOMAL PROTEIN L16"},"ncbifam":{"TIGR01164":"50S ribosomal protein L16"},"prints":{"PR00060":"RIBOSOMALL16"}},"go_terms":[{"identifier":"GO:0003735","name":"structural constituent of ribosome","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0019843","name":"rRNA binding","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0006412","name":"translation","category":{"code":"P","name":"biological_process"}}]},"extra_fields":{"description":[{"text":"Ribosomal protein uL16 is one of the proteins from the large ribosomal subunit from bacteria and its homologues from chloroplast and mitochondria. In Escherichia coli, uL16 is known to bind directly the 23S rRNA and to be located at the A site of the peptidyltransferase centre. uL16 is a protein of 133 to 185 amino-acid residues.
","llm":false,"checked":false,"updated":false},{"text":"Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA, and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid of the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [[cite:PUB00007068], [cite:PUB00007069]]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 consists of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to: the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.
\n\nMany ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waals' contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way, proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA-based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [[cite:PUB00007069], [cite:PUB00007070]].
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000115","name":"Phosphoribosylglycinamide synthetase","source_database":"interpro","type":"family","integrated":null,"member_databases":{"panther":{"PTHR43472":"PHOSPHORIBOSYLAMINE--GLYCINE LIGASE"},"hamap":{"MF_00138":"Phosphoribosylamine--glycine ligase [purD]"},"ncbifam":{"TIGR00877":"phosphoribosylamine--glycine ligase"}},"go_terms":[{"identifier":"GO:0004637","name":"phosphoribosylamine-glycine ligase activity","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0009113","name":"purine nucleobase biosynthetic process","category":{"code":"P","name":"biological_process"}}]},"extra_fields":{"description":[{"text":"Phosphoribosylglycinamide synthetase ([ec:6.3.4.13]) (GARS) (phosphoribosylamine glycine ligase) [[cite:PUB00002527]] catalyses the second step in thede novobiosynthesis of purine. The reaction catalysed by phosphoribosylglycinamide synthetase is the ATP-dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide:
\n\n\n
In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5,7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) [[cite:PUB00075625]]. In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS and with phosphoribosylglycinamide formyltransferase (GART), forming GARS-AIRS-GART [[cite:PUB00075622]].
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000131","name":"ATP synthase, F1 complex, gamma subunit","source_database":"interpro","type":"family","integrated":null,"member_databases":{"cdd":{"cd12151":"mitochondrial ATP synthase gamma subunit"},"hamap":{"MF_00815":"ATP synthase gamma chain [atpG]"},"ncbifam":{"TIGR01146":"ATP synthase F1 subunit gamma"},"panther":{"PTHR11693":"ATP SYNTHASE GAMMA CHAIN"},"pfam":{"PF00231":"ATP synthase"},"prints":{"PR00126":"ATPASEGAMMA"}},"go_terms":[{"identifier":"GO:0046933","name":"proton-transporting ATP synthase activity, rotational mechanism","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0015986","name":"proton motive force-driven ATP synthesis","category":{"code":"P","name":"biological_process"}},{"identifier":"GO:0045259","name":"proton-transporting ATP synthase complex","category":{"code":"C","name":"cellular_component"}}]},"extra_fields":{"description":[{"text":"The ATPase F1 complex gamma subunit forms the central shaft that connects the F0 rotary motor to the F1 catalytic core. The gamma subunit functions as a rotary motor inside the cylinder formed by the α(3)β(3) subunits in the F1 complex [[cite:PUB00020605]]. The most conserved region of the gamma subunit is its C terminus, which seems to be essential for assembly and catalysis.
","llm":false,"checked":false,"updated":false},{"text":"F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) ([ec:7.1.2.2]) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the α(3)β(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis [[cite:PUB00009752]]. These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.
","llm":false,"checked":false,"updated":false},{"text":"Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000146","name":"Fructose-1,6-bisphosphatase class 1","source_database":"interpro","type":"family","integrated":null,"member_databases":{"pirsf":{"PIRSF000904":"Fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase"},"panther":{"PTHR11556":"FRUCTOSE-1,6-BISPHOSPHATASE-RELATED"},"cdd":{"cd00354":"FBPase"},"hamap":{"MF_01855":"Fructose-1,6-bisphosphatase class 1 [fbp]"}},"go_terms":[{"identifier":"GO:0016791","name":"phosphatase activity","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0005975","name":"carbohydrate metabolic process","category":{"code":"P","name":"biological_process"}}]},"extra_fields":{"description":[{"text":"This entry represents the fructose-1,6-bisphosphatase (FBPase) class 1 family. FBPase is a critical regulatory enzyme in gluconeogenesis that catalyses the removal of 1-phosphate from fructose 1,6-bis-phosphate to form fructose 6-phosphate [[cite:PUB00000153], [cite:PUB00000179]]. It is involved in many different metabolic pathways and found in most organisms. FBPase requires metal ions for catalysis (Mg2+and Mn2+being preferred) and the enzyme is potently inhibited by Li+. The fold of fructose-1,6-bisphosphatase was noted to be identical to that of inositol-1-phosphatase (IMPase) [[cite:PUB00000219]]. Inositol polyphosphate 1-phosphatase (IPPase), IMPase and FBPase share a sequence motif (Asp-Pro-Ile/Leu-Asp-Gly/Ser-Thr/Ser) which has been shown to bind metal ions and participate in catalysis. This motif is also found in the distantly-related fungal, bacterial and yeast IMPase homologues. It has been suggested that these proteins define an ancient structurally conserved family involved in diverse metabolic pathways, including inositol signalling, gluconeogenesis, sulphate assimilation and possibly quinone metabolism [[cite:PUB00004864]].
\r\nThis entry also includes sedoheptulose-1,7-bisphosphatase, which is a member of the FBPase class 1 family.
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000148","name":"Papillomavirus E7","source_database":"interpro","type":"family","integrated":null,"member_databases":{"hamap":{"MF_04004":"Protein E7 [E7]"},"pfam":{"PF00527":"E7 protein, Early protein"},"pirsf":{"PIRSF003407":"Transforming protein E7, Papillomavirus type"}},"go_terms":[{"identifier":"GO:0003677","name":"DNA binding","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0003700","name":"DNA-binding transcription factor activity","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0006355","name":"regulation of DNA-templated transcription","category":{"code":"P","name":"biological_process"}}]},"extra_fields":{"description":[{"text":"This family includes the E7 oncoprotein from various papillomaviruses [[cite:PUB00009552]]. Along with E5 and E6 their activities seem to be especially important for viral oncogenesis. E5 is located at the cell surface and reduces cell gap-gap junction communication. In cervical cancer E5 is expressed in earlier stages of neoplastic transformation of the cervical epithelium during viral infection. The role of E7 is less well understood but it has been shown to impede growth arrest signals in both NIH 3T3 cells and HFKs and that this correlates with elevated cdc25A gene expression. This deregulation of cdc25A is linked to disruption of cell cycle arrest [[cite:PUB00009553]].
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000158","name":"Cell division protein FtsZ","source_database":"interpro","type":"family","integrated":null,"member_databases":{"hamap":{"MF_00909":"Cell division protein FtsZ [ftsZ]"},"cdd":{"cd02201":"Filamenting temperature sensitive mutant Z, type 1"},"ncbifam":{"TIGR00065":"cell division protein FtsZ"}},"go_terms":[{"identifier":"GO:0003924","name":"GTPase activity","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0005525","name":"GTP binding","category":{"code":"F","name":"molecular_function"}}]},"extra_fields":{"description":[{"text":"In bacteria, FtsZ [[cite:PUB00003846], [cite:PUB00000910], [cite:PUB00007093], [cite:PUB00074277]] is an essential cell division protein involved in the initiation of this event. It assembles into a cytokinetic ring on the inner surface of the cytoplasmic membrane at the place where division will occur. The ring serves as a scaffold that is disassembled when septation is completed. FtsZ ring formation is initiated at a single site on one side of the bacterium and appears to grow bidirectionally. In Escherichia coli, MinCD [interpro:IPR005526], encoded by the MinB locus, form a complex which appears to block the formation of FtsZ rings at the cell poles, at the ancient mid cell division sites, whilst MinE, encoded at the same locus, specifically prevents the action of MinCD at mid cell.
\n\nFtsZ is a GTP binding protein with a GTPase activity. It undergoes GTP-dependent polymerisation into filaments (or tubules) that seem to form a cytoskeleton involved in septum synthesis. The structure and the properties of FtsZ clearly provide it with the capacity for the cytoskeletal, perhaps motor role, necessary for \"contraction\" along the division plane. In addition, however, the FtsZ ring structure provides the framework for the recruitment or assembly of the ten or so membrane and cytoplasmic proteins, uniquely required for cell division in E. coli or Bacillus subtilis, some of which are required for biogenesis of the new hemispherical poles of the two daughter cells. FtsZ can polymerise into various structures, for example a single linear polymer of FtsZ monomers, called a protofilament. Protofilaments can associate laterally to form pairs (sometimes called thick filaments), bundles (ill-defined linear associations of multiple protofilaments) or thick filaments, sheets (parallel or anti-parallel two-dimensional associations of thick filaments) and tubes (anti-parallel associations of thick filaments in a circular fashion to form a tubular structure). In addition, small circles of FtsZ monomers (a short protofilament bent around to join itself, apparently head to tail) have been observed and termed mini-rings.
\n\nFtsZ is a protein of about 400 residues which is well conserved across bacterial species and which is also present in the chloroplast of plants [[cite:PUB00004215]] as well as in archaebacteria [[cite:PUB00002291]]. FtsZ is a homologue of eukaryotic tubulin with which it shows structural similarity.
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000178","name":"Translation initiation factor IF-2, bacterial-like","source_database":"interpro","type":"family","integrated":null,"member_databases":{"prosite":{"PS01176":"Initiation factor 2 signature"},"hamap":{"MF_00100_B":"Translation initiation factor IF-2 [infB]"},"ncbifam":{"TIGR00487":"translation initiation factor IF-2"}},"go_terms":[{"identifier":"GO:0003743","name":"translation initiation factor activity","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0003924","name":"GTPase activity","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0005525","name":"GTP binding","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0006413","name":"translational initiation","category":{"code":"P","name":"biological_process"}}]},"extra_fields":{"description":[{"text":"Initiation factor 2 (IF-2) (gene infB) [[cite:PUB00000691]] is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-2 promotes the GTP-dependent binding of the initiator tRNA to the small subunit of the ribosome. IF-2 is a protein of about 70 to 95 Kd which contains a central GTP-binding domain flanked by a highly variable N-terminal domain and a more conserved C-terminal domain. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial IF-2 (IF-2(mt)) [[cite:PUB00002916]] as well as to algal and plants chloroplast IF-2 (IF-2(chl)). Both IF-2(mt) and IF-2(chl) are encoded by nuclear genes and are produced as precursor proteins with a transit peptide. An exception are red algae where IF-2(chl) is encoded by the plastid genome [[cite:PUB00004567]].
","llm":false,"checked":false,"updated":false},{"text":"This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognised by the pfam HMM GTP_EFTU.
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000185","name":"Protein translocase subunit SecA","source_database":"interpro","type":"family","integrated":null,"member_databases":{"panther":{"PTHR30612":"SECA INNER MEMBRANE COMPONENT OF SEC PROTEIN SECRETION SYSTEM"},"hamap":{"MF_01382":"Protein translocase subunit SecA [secA]"},"prints":{"PR00906":"SECA"},"ncbifam":{"TIGR00963":"preprotein translocase subunit SecA"}},"go_terms":[{"identifier":"GO:0005524","name":"ATP binding","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0006605","name":"protein targeting","category":{"code":"P","name":"biological_process"}},{"identifier":"GO:0006886","name":"intracellular protein transport","category":{"code":"P","name":"biological_process"}}]},"extra_fields":{"description":[{"text":"Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component [[cite:PUB00007064]]. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.
\n\nThe translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) [[cite:PUB00007064]]. The chaperone protein SecB [[cite:PUB00007065]] is a highly acidic homotetrameric protein that exists as a \"dimer of dimers\" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion [[cite:PUB00007066]].
\n\nSecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologues of secA are also encoded in the chloroplast genome of some algae [[cite:PUB00003757]] as well as in the nuclear genome of plants [[cite:PUB00001687]]. It could be involved in the intraorganellar protein transport into thylakoids.
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000196","name":"Large ribosomal subunit protein eL19 domain","source_database":"interpro","type":"domain","integrated":null,"member_databases":{"ncbifam":{"NF006343":"50S ribosomal protein L19e"},"smart":{"SM01416":"Ribosomal_L19e"},"hamap":{"MF_01475":"Large ribosomal subunit protein eL19 [rpl19e]"}},"go_terms":[{"identifier":"GO:0003735","name":"structural constituent of ribosome","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0006412","name":"translation","category":{"code":"P","name":"biological_process"}},{"identifier":"GO:0005840","name":"ribosome","category":{"code":"C","name":"cellular_component"}}]},"extra_fields":{"description":[{"text":"This entry represents a structural domain of large ribosomal subunit protein eL19, found in archaea and eukaryotes [[cite:PUB00006505], [cite:PUB00030943], [cite:PUB00080279]].
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000206","name":"Large ribosomal subunit protein bL12","source_database":"interpro","type":"family","integrated":null,"member_databases":{"cdd":{"cd00387":"Ribosomal_L7_L12"},"hamap":{"MF_00368":"Large ribosomal subunit protein bL12 [rplL]"},"panther":{"PTHR45987":"39S RIBOSOMAL PROTEIN L12"},"ncbifam":{"TIGR00855":"50S ribosomal protein L7/L12"}},"go_terms":[{"identifier":"GO:0003735","name":"structural constituent of ribosome","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0006412","name":"translation","category":{"code":"P","name":"biological_process"}},{"identifier":"GO:0005840","name":"ribosome","category":{"code":"C","name":"cellular_component"}}]},"extra_fields":{"description":[{"text":"This family represents the large ribosomal subunit protein bL12, formerly known as L7/L12 in E. coli (L7 and L12 are identical except that L7 is acetylated at the N terminus) [[cite:PUB00080279]]. This protein is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of bL12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain [[cite:PUB00006172]]. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for bL12. bL12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. bL12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of bL12 are highly mobile. They are exposed to the cytoplasm and contain binding sites for other molecules. Initiation factors, elongation factors, and release factors are known to interact with the L7/L12 stalk during their GTP-dependent cycles. The binding site for the factors EF-Tu and EF-G comprises bL12, L10, L11, the L11-binding region of 23S rRNA, and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12 has minimal effect on factor binding and it has been proposed that bL12 induces the catalytically active conformation of EF-Tu and EF-G, thereby stimulating the GTPase activity of both factors [[cite:PUB00079605], [cite:PUB00079606], [cite:PUB00079607], [cite:PUB00007069], [cite:PUB00007070], [cite:PUB00016781], [cite:PUB00038823], [cite:PUB00039608], [cite:PUB00079608], [cite:PUB00037548], [cite:PUB00079609], [cite:PUB00079611], [cite:PUB00079612], [cite:PUB00025269], [cite:PUB00010619], [cite:PUB00003217], [cite:PUB00079613]].
\n\nIn eukaryotes, the proteins that perform the equivalent function to bL12 are called P1 and P2, which do not share sequence similarity with these proteins. However, a bacterial bL12 homologue is found in some eukaryotes, in mitochondria and chloroplasts [[cite:PUB00079610]]. In archaea, the protein equivalent to bL12 is called aL12 or L12p, but it is closer in sequence to P1 and P2 than to bL12 [[cite:PUB00045897]].
","llm":false,"checked":false,"updated":false},{"text":"Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA, and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid of the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [[cite:PUB00007068], [cite:PUB00007069]]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 consists of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to: the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.
\n\nMany ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waals' contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way, proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA-based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [[cite:PUB00007069], [cite:PUB00007070]].
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000218","name":"Large ribosomal subunit protein uL14","source_database":"interpro","type":"family","integrated":null,"member_databases":{"smart":{"SM01374":"Ribosomal protein L14p/L23e"},"hamap":{"MF_01367":"Large ribosomal subunit protein uL14 [rplN]"},"panther":{"PTHR11761":"50S/60S RIBOSOMAL PROTEIN L14/L23"},"pfam":{"PF00238":"Ribosomal protein L14p/L23e"}},"go_terms":[{"identifier":"GO:0003735","name":"structural constituent of ribosome","category":{"code":"F","name":"molecular_function"}},{"identifier":"GO:0006412","name":"translation","category":{"code":"P","name":"biological_process"}},{"identifier":"GO:0005840","name":"ribosome","category":{"code":"C","name":"cellular_component"}}]},"extra_fields":{"description":[{"text":"This entry represents the large ribosomal subunit protein uL14 (formerly known as L14) from all domains of life. In eubacteria, uL14 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins, which have been grouped on the basis of sequence similarities. Based on amino-acid sequence homology, it is predicted that ribosomal protein L14 is a member of a recently identified family of structurally related RNA-binding proteins [[cite:PUB00015240]]. L14 is a protein of 119 to 137 amino-acid residues.
","llm":false,"checked":false,"updated":false},{"text":"Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA, and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid of the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [[cite:PUB00007068], [cite:PUB00007069]]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 consists of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to: the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.
\n\nMany ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waals' contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way, proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA-based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [[cite:PUB00007069], [cite:PUB00007070]].
","llm":false,"checked":false,"updated":false}]}},{"metadata":{"accession":"IPR000229","name":"Nucleocapsid protein, arenaviridae","source_database":"interpro","type":"family","integrated":null,"member_databases":{"hamap":{"MF_04085":"Nucleoprotein [N]"},"pirsf":{"PIRSF004029":"Nucleocapsid protein, Arenaviridae type"}},"go_terms":[{"identifier":"GO:0019013","name":"viral nucleocapsid","category":{"code":"C","name":"cellular_component"}}]},"extra_fields":{"description":[{"text":"Arenaviridae are single stranded RNA viruses. The arenaviridae S RNAs that have been characterised include conserved terminal sequences, an ambisense arrangement of the coding regions for the precursor glycoprotein (GPC) and nucleocapsid (N) proteins and an intergenic region capable of forming a base-paired \"hairpin\" structure. The mature glycoproteins that result are G1 and G2 and the N protein [[cite:PUB00006263]].
","llm":false,"checked":false,"updated":false},{"text":"This family represents the nucleocapsid protein that encapsulates the viral ssRNA [[cite:PUB00005615]].
","llm":false,"checked":false,"updated":false}]}}]}